Tag Archives: yeast

Open Notebook, Water Analysis, Water Type Effects on Organism Growth

Project planning notes via Handrite

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Here are some notes I took using handrite for android regarding my project plans. I don’t mean to advertise for anything, but I use this app ALL THE TIME and it is super helpful. Typing on my phone is annoying sometimes and Handrite allows me to use my finger to write (albeit sloppily). These notes were taken yesterday while I was meeting with Steve (on my phone) and now I have time to paste them in my notebook. So here is some background on my ramblings:

  • I would like to effectively analyze the amount of hydrogen-deuterium exchange in my samples. This is a phenomenon I’ve talked about a lot, know very little about, and stress a lot over. We tried FT-IR of water samples to see if we can determine differences in the water types. We’ve had mixed results in this regard. It boils down to the fact, that I don’t trust anything. How do I know that deuterium isn’t sneaking into my unopened bottles of DDW, or that hydrogen isn’t getting into my D2O? What about after it’s been opened? What about in my samples? If I’m going to get reliable results with yeast and e. coli I’ll need to know if I can trust commercial products.
  • NMR (nuclear magnetic resonance) seems to be a promising route to try and there may be some equipment either in the Chemistry department or Biomedical Engineering here at UNM that I’ll need to look into.
  • Mass spectrometry may be another avenue to determine precise amounts of deuterium in water.
  • Something not written but that I talked with Steve about yesterday and just remembered is that I need to talk with Sigma to find out how they measure the purity of the DDW and how reliable those measurements are long term. If something sits on a shelf for a year, how do I know it isn’t really just pure natural water?
  • I also have some stuff in my notes about the Repeating Crumley experiment. I just setup a D2O only experiment to show definitively that tobacco seeds do not grow in D2O. Previously I would only track this data for 10-15 days and Crumley went up to a month (if I remember correctly). I’ll write the setup in a minute, but I want to do 30 days so I have some pictures for my open access, self published RC paper (spoiler alert!).
  • Also to show that I’m no slouch, I want to try and repeat Crumley’s original experiment with paper towels to show that the growth of the 100% D2O seeds was due to H-D exchange and other environmental factors and not because they eventually grow in D2O. Yea I’m a badass.
  • The rest of the notes are some ramblings that are not really private but thoughts I would prefer not to elaborate on now.

Tata for now!

Ecoli1, Open Notebook, Water Type Effects on Organism Growth, Yeast1

#SciFund Challenge Accepted!

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If you watch “How I Met Your Mother” you’ll get the title of this post. But if you don’t then I’ll let it be known that I have just completed my submission for the second #SciFund challenge which is hosted by RocketHub.com. Here is my submission:


Effects of DDW on Microorganisms

Genomic Data, KochLab Stuff, Shotgun DNA Mapping

DNA sequences for Shotgun DNA Mapping Algorithms

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Via Dropbox:

If I can think of other cool things to download and upload to dropbox I’ll add them here.

Genomic Data, Shotgun DNA Mapping

Yeast genome found… potentially

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Ok so yeastgenome.org was kinda complicated to navigate, but once I noticed a handy little link on the top of the site named “Download” then it was much easier. Here are some notes:

  • From the main page click Download. Then click Sequence. On that page is a list of genomes that aren’t S. cerevisiae (something cool for later maybe), and a list of sequence files that are of the reference strain S288C (which I have no understanding of).
  • On that page I clicked genomic_releases/ to get a list of updates for the yeast genome. I’m thinking Larry probably downloaded the most recent at the time which is from June 5, 2008, but I can also see him just picking whatever is at the top (which may have been the same file, it is only labeled “Current Release”).
  • I realize I could have just linked one of those links, but what kind of notebook would this be if I didn’t show you my entire train of thought? A shitty one, that’s what kind!
  • You will need 7-zip to open the downloaded sequence because it is saved as a “.tzg”.
  • I’m also downloading the most recent update to the genome, maybe this will be useful for the matching aspect of the simulation. The date on this file is Feb 3, 2011.
Genomic Data, Shotgun DNA Mapping

Navigating Larry’s notebook and finding yeast genome

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The link to Larry’s notebook (pertaining to SDM) is here (this is on a private site, sorry!). His notebook is terribly organized, so going through this takes some time. He does have a public notebook, but that is mostly about microtubule tracking software and kinesin motility simulations.

screenshots of larry's notebook displayed as a calendar.

For your benefits here is a picture of his private notebook. On the right is the 2008 notebook where the information I’m looking for resides. The left is from 2009 which contains information about upgrades and side projects to SDM. For instance the first entry of the year discusses some preliminary research regarding inversions for an application into SDM known as alternative splicing. The last entry of the year (because Larry went public) talks about some upgrades to the original simulation software, basically incorporating some more advanced mathematics into the unzipping energies.

From what I remember about 2008, Larry started designing the software we needed for SDM around July/August so I’ll start there. The paper was submitted to Nature Preceedings January 2009 to give you some scope.

Ok looking through starting Aug 1, I found this (August 6, 2008). This marks the first appearance of anything related to SDM. For those with no access here:

On that page there is a link to yeastgenome.org and Larry talks about how he can’t navigate the site and has no clue what he is doing. I’m guessing things have changed considerably in 3.5 years as I just went there and easily found a list of complete genome sequences for 28 strains of S. cerevisiae. Hoepfully as I look through Larry’s notes I’ll find exactly which strain he downloaded, otherwise I’ll just have to figure something out. Now it’s time to look through his notes and find important stuff. I’ll be back.

Genomic Data, Shotgun DNA Mapping

Finding the yeast genome

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Today my goal is to acquire some genetic sequences for use in the algorithm. Once we get the software up and running, implementing this stuff should be simple. The goal for Steve today is to get that software up and running.

First I need to find Larry’s private wiki notes about where he got the yeast genome from and how he used it. I’ll be creating new posts (since I don’t think updating this post will be adequate or appropriate, it’s a my brain kinda thing) regarding this task as I progress throughout the day.

And I’ll be starting with Larry’s notes, by making relevant stuff public here. Avante!

Water Type Effects on Organism Growth, Yeast1

Yeast Update

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I realized that I left stuff in the incubator all through the weekend into today. When I checked my samples, there was a ton of growth. So much so that the cultures on the dish were 3D and the liquid culture I had had some amorphous yeast blob on the bottom. It was pretty crazy. I poured that stuff down the drain and I’ll make a new culture in the morning (since I won’t be here tomorrow afternoon to check it out, plus I’m out of autoclaved test tubes).

Ecoli1, Water Type Effects on Organism Growth, Yeast1

Yeast: Day 2

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So my overnight culture grew, that’s cool. The E coli did not though. That’s not. To make matters worse, the -80C freezer had some weird malfunction and it was nearly RT in there. Hopefully nothing is ruined. I’ll restart experiments on Monday and make new batches of yeast and e coli spreads and liquid media as well. Then I’ll make some glycerol stocks so that I can be ready for all eternity.

On top of all that I’ll reacquaint myself with doing transformations and purifying plasmids because there are some vectors that I need to replenish. Not for the purposes of these experiments, but just because.

I’ll try and do some preplanning over the weekend and through Monday.

Water Type Effects on Organism Growth, Yeast1

Yeast cultures

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We streaked two plates and poured a bunch of stock into the third plate (hence the whole lotta cells). I didn’t do the streaking because they weren’t my cells.

I did pick a colony from the third plate and streaked that onto a new plate, so hopefully there will be good spreading.

I parafilmed the plates and stuck them in the fridge.

Onward to tomorrow.